In-depth transcriptome analysis reveals novel TARs and prevalent antisense transcription in human cell lines.

• Several recent studies have indicated that transcription is pervasive in regions outside of protein coding genes and that short antisense transcripts can originate from the promoter and terminator regions of genes. Here we investigate transcription of fragments longer than 200 nucleotides, focusing on antisense transcription for known protein coding genes and intergenic transcription. We find that roughly 12% to 16% of all reads that originate from promoter and terminator regions, respectively, map antisense to the gene in question. Furthermore, we detect a high number of novel transcriptionally active regions (TARs) that are generally expressed at a lower level than protein coding genes. We also investigate the correlation between RNA-seq data and microarray data and conclude that the correlation is dependant on gene length such that longer genes show a better correlation.

Subject headings

NATURVETENSKAP  -- Biologi -- Annan biologi (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences -- Other Biological Topics (hsv//eng)

Keyword

Transcriptome

non-coding RNA

DNA sequencing

next generation sequencing

Functional genomics

Funktionsgenomik

Publication and Content Type

vet (subject category)

ovr (subject category)